if not path.isdir(results_dir):
# Create the results folder if it doesn't exist
os.makedirs(results_dir)
files = os.listdir(files_dir)
types_delete = [97, 98, 99, 100]
types_replace = {
94: 84,
96: 85,
101: 34,
102: 86,
103: 88
}
for file_name in files:
if Util.get_file_extension(file_name) != ".xml":
continue
p = path.join(files_dir, file_name)
print ("Processing {0}...".format(file_name))
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
geom.num_dimensions = 3
points = []
change_coords = geom.coordinate_system != geom.LPS
for point[ in geom.points:
if point.chest_type not in types_delete:
if types_replace.has_key(point.chest_type):
# Replace type
point.chest_type = types_replace[point.chest_type]
if change_coords:
sys.path.append("/Users/jonieva/Projects/SlicerCIP/Scripted/CIP_Common/")
from CIP.logic import geometry_topology_data as gtd
from CIP.logic import Util
import os
import os.path
import re
wrong_cases_path = "/Volumes/Mac500/Dropbox/rola-jorge/LH ROI failure/"
xmls_path = "/Volumes/Mac500/Dropbox/ACIL-Biomarkers/parenchyma training 2015-10-02/"
results_path = "/Volumes/Mac500/Data/tempdata/parenchyma training 2015-10-02/Removed Points/LH ROI failure"
current_case = ""
caseIds = dict()
for file_name in os.listdir(wrong_cases_path):
if Util.get_file_extension(file_name) != ".png":
continue
expr = "(?P<caseid>(^(.*?)_(.*?)_(.*?)_(.*?)_(.*?)))_(.*?)_p(?P<point>(.*?))_(.*)"
r = re.match(expr, file_name)
caseId = r.group("caseid")
point = int(r.group("point"))
if not caseIds.has_key(caseId):
caseIds[caseId] = []
caseIds[caseId].append(point)
for caseId, excludedPoints in caseIds.iteritems():
# Load the Geometry object
geom = gtd.GeometryTopologyData.from_xml_file(os.path.join(xmls_path, caseId + "_parenchymaTraining.xml"))
newPoints=[]
for i in range(len(geom.points)):
if i not in excludedPoints:
if not path.isdir(results_dir):
# Create the results folder if it doesn't exist
os.makedirs(results_dir)
files = os.listdir(files_dir)
types_delete = [97, 98, 99, 100]
types_replace = {
94: 84,
96: 85,
101: 34,
102: 86,
103: 88
}
for file_name in files:
if Util.get_file_extension(file_name) != ".xml":
continue
p = path.join(files_dir, file_name)
print ("Processing {0}...".format(file_name))
with open(p, "r+b") as f:
xml = f.read()
geom = gtd.GeometryTopologyData.from_xml(xml)
geom.num_dimensions = 3
points = []
change_coords = geom.coordinate_system != geom.LPS
for point in geom.points:
if point.chest_type not in types_delete:
if types_replace.has_key(point.chest_type):
# Replace type
point.chest_type = types_replace[point.chest_type]
if change_coords:
sys.path.append("/Users/jonieva/Projects/SlicerCIP/Scripted/CIP_Common/")
from CIP.logic import geometry_topology_data as gtd
from CIP.logic import Util
import os
import os.path
import re
wrong_cases_path = "/Volumes/Mac500/Dropbox/rola-jorge/LH ROI failure/"
xmls_path = "/Volumes/Mac500/Dropbox/ACIL-Biomarkers/parenchyma training 2015-10-02/"
results_path = "/Volumes/Mac500/Data/tempdata/parenchyma training 2015-10-02/Removed Points/LH ROI failure"
current_case = ""
caseIds = dict()
for file_name in os.listdir(wrong_cases_path):
if Util.get_file_extension(file_name) != ".png":
continue
expr = "(?P<caseid>(^(.*?)_(.*?)_(.*?)_(.*?)_(.*?)))_(.*?)_p(?P<point>(.*?))_(.*)"
r = re.match(expr, file_name)
caseId = r.group("caseid")
point = int(r.group("point"))
if not caseIds.has_key(caseId):
caseIds[caseId] = []
caseIds[caseId].append(point)
for caseId, excludedPoints in caseIds.iteritems():
# Load the Geometry object
geom = gtd.GeometryTopologyData.from_xml_file(
os.path.join(xmls_path, caseId + "_parenchymaTraining.xml"))
newPoints = []
for i in range(len(geom.points)):
